Directory and doc rules
knitr::opts_chunk$set(
echo = FALSE, # Display code chunks
eval = TRUE, # Evaluate code chunks
warning = FALSE, # Hide warnings
message = FALSE, # Hide messages
fig.width = 20, # Set plot width in inches
fig.height = 15, # Set plot height in inches
fig.align = "center" )# Align plots to the center
Load data
p450
dumbbell - original data in alphabetical order
dumbbell - PAH group 8
## Kruskal-Wallis rank sum test
##
## data: x and group
## Kruskal-Wallis chi-squared = 30.4644, df = 8, p-value = 0
##
##
## Comparison of x by group
## (Bonferroni)
## Col Mean-|
## Row Mean | 10 11 12 13 6 7
## ---------+------------------------------------------------------------------
## 11 | -1.949000
## | 0.9233
## |
## 12 | 2.580192 3.392567
## | 0.1777 0.0125*
## |
## 13 | -3.481090 -1.464937 -4.069711
## | 0.0090* 1.0000 0.0008*
## |
## 6 | -0.441923 0.770017 -2.515655 1.736194
## | 1.0000 1.0000 0.2139 1.0000
## |
## 7 | -0.101305 1.500658 -2.515347 2.771326 0.336028
## | 1.0000 1.0000 0.2140 0.1005 1.0000
## |
## 8.1 | -0.410541 0.494120 -2.262756 1.221145 -0.071786 -0.337834
## | 1.0000 1.0000 0.4257 1.0000 1.0000 1.0000
## |
## 8.2 | -2.770580 -1.432479 -3.915137 -0.407957 -1.757716 -2.441850
## | 0.1007 1.0000 0.0016* 1.0000 1.0000 0.2630
## |
## 9 | -0.392586 1.018006 -2.584874 2.137008 0.091831 -0.270661
## | 1.0000 1.0000 0.1753 0.5868 1.0000 1.0000
## Col Mean-|
## Row Mean | 8.1 8.2
## ---------+----------------------
## 8.2 | -1.348148
## | 1.0000
## |
## 9 | 0.148740 2.031964
## | 1.0000 0.7588
##
## alpha = 0.05
## Reject Ho if p <= alpha/2
box plot - site
boxplot - reporting area
boxplot - PAH group 8
fix plotting order - it’s backwards
boxplot significant comparison code - haven’t checked it
correlation plot
correlation table
## analyte correlation p_value
## 1 avg_sod -0.326 0.005
## 2 a7 0.229 0.050
## 3 a12 0.233 0.046
## 4 a14 0.233 0.046
## 5 a15 0.256 0.028
## 6 a17 0.233 0.046
## 7 a18 0.233 0.046
## 8 a19 0.229 0.050
## 9 a63 0.233 0.046
## 10 a74 0.261 0.025
## 11 a81 0.254 0.029
## 12 a120 0.259 0.026
## 13 a125 -0.282 0.015
linear regression - signficant analytes
